Unfortunately I don't have a lot of information regarding the stutter issue. -Out of curiosity, have you tried disabling the AI changes the mod makes? That's the primary culprit I can think of, once you're sure it's not a "Too many bots" issue. I'll try and look into this a bit more myself, but in the past this has been an ellusive issue that doesn't seem to affect all SPT installations equally.
That's one of the first things I tried was disabling AI spawn changes, however I didn't disable the "all AI changes" feature on the config editor exe because I wasn't sure if this option affected difficulty changes (which is why I got the mod in the first place). I then tried running Lua spawn rework alongside to see if I could use Lua for the spawns and use FAIT for things like gear changes and difficulty. It didn't seem to matter though, I still experienced stutters and freezes.
I also tried disabling some of the features I circled in the picture shown here. These were some of the configs I had a hunch may have been a cause but they don't seem to change much in performance at least for me.